Direct Censoring with 3dREMLfit

Dear Colleagues,

Catie Chang and I would like to use 3dREMLfit to regress out cardiac and respiratory phase by slice with the -slibase option. Catie is generating the .1D input matrix that is necessary for this option with a custom Matlab routine.

Because we are not using 3dDeconvolve to generate the input matrix, which would also contain the censoring, can a -censor option be used directly in 3dREMLfit? If yes, even though we are correcting by slice, can the censor file be in TRs, or would it need to be upsampled according to the number of slices per volume? If no, how might we proceed? Thank you.

Sincerely,

Dante

Hi Dante,

We do not give the slice-based regressors to 3dDeconvolve in any
case (it has no ability to handle them). Just use 3dDeconvolve to
generate the rest of the matrix, pass it to 3dREMLfit, and add the
appropriate -slibase* option to 3dREMLfit with your generated
slice-based regressors. The matrix that you pass from 3dD to
3dR will have the censoring information.

  • rick
1 Like

Rick,

Thank you very much as always.

Sincerely,

Dante